Reverse vaccinology assisted design of a novel multi-epitope vaccine to target Wuchereria bancrofti cystatin: An immunoinformatics approach

Cell Surface Fibroblast Activation Protein-2 (Fap2) of Fusobacterium nucleatum as a Vaccine Candidate for Therapeutic Intervention of Human Colorectal Cancer: An Immunoinformatics Approach

“…The complete sequence of the F. nucleatum Fap2 protein (3799 amino acids) was retrieved in FASTA format from the National Centre for Biotechnological Information (NCBI) ( , accessed on 14 January 2023) protein database (accession number: WP016361450.1) and was used for the study. The FBCPred ( , accessed on 14 January 2023) and ABCPred ( , accessed on 14 January 2023) servers were explored to determine the B-cell epitopes present in the Fap2 protein and were further used to screen the common epitopes [ 22 , 23 ].…”

“…3A79_C). Secondary structures of all the vaccine candidates were determined using the two feed-forward neural network methods provided in the PSIPRED 4.0 server ( , accessed on 14 January 2023), and all the structures were refined following earlier reports [ 22 , 29 ].…”

“…The binding affinity of each vaccine construct toward the different TLRs was studied using molecular docking analysis. The 3D structures of different TLRs, viz., TLR1/TLR2, TLR4–MD2 complex, and TLR5 were retrieved from RCSB protein databank ( , accessed on 14 January 2023) while TLR6 was modelled following our previous reports [ 22 , 29 , 35 ]. All the structures were refined and validated before performing the molecular docking.…”

“…In addition to NMA, molecular dynamics (MD) simulation trajectory analysis was performed using GROMACSv5.1 package (GROningenMAchine for Chemical Simulations) to cross-verify the structural stability of the vaccine–TLR complexes [ 22 , 35 ]. To construct the configuration of the docked complexes, the pdb2gmx module and force field gromos96 53a6 were used [ 22 , 35 ]. The system was then placed in a cubical box and solvated using a simple point charge (SPC) water model that exploited the editconf and solvate modules.…”

“…Finally, MD prediction was accomplished using timesteps of 10 ns for a total span of 100 ns. Grace 5.1.23 was used to plot the simulation data in different graphs, such as the root–mean–square fluctuation (RMSF), root–mean–square deviation (RMSD), a radius of gyration (Rg), and solvent accessible surface area (SASA) [ 22 , 35 ]. The conformational changes within each vaccine–TLR complex throughout the MDS process were determined by superimposing the simulated docked structures obtained from the different phases of the simulation study.…”